RnoINT0158237 @ rn6
Intron Retention
Gene
ENSRNOG00000047505 | Tubb4a
Description
tubulin, beta 4A class IVa [Source:RGD Symbol;Acc:619730]
Coordinates
chr9:9961021-9962366:+
Coord C1 exon
chr9:9961021-9961189
Coord A exon
chr9:9961190-9962257
Coord C2 exon
chr9:9962258-9962366
Length
1068 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGC
5' ss Score
10.4
3' ss Seq
CCCTCTTCCCCATCCTCTAGTTC
3' ss Score
10.03
Exon sequences
Seq C1 exon
TAGAGACGCCCGGGGGCGCAGAGACAGAGCTCTGCAGCCATCTCCTCCAGAGACGGAACCACAGCGACCGGTTGACACCCGTCCATCAGCCGCCACCAGCAGCACCCCCATCATGCGGGAAATCGTGCACCTGCAAGCCGGGCAATGCGGCAACCAGATCGGGGCCAAG
Seq A exon
GTACGCCAGGCTGGGTAACGGGGTGGGGATGCAGAGGGGCTCGGAAATGGCTCCTTGGCTCCCCCAAGACTCGCCCAGGAATTCTGCATCCCAGGTGGAGGAGGGGAGCCAGGGCAGAGGCACACTGGGAACAAAGAGGCTGATGATGGGGGCAGGGCCTGGCCTTGTGTCCCTTGGCCACAGCTGGCCTCACAGCTGGGCCACTGTCACCCTCAGTTGCCCGGCACAAAGAGGCACGGCCCCTCCTCCCAGGGCTGCTGCTGGGATAGACTGGCACCAAGTGGCTCTGGTGGGGGCCAAGCTTCTCCCTACCCCCAACTTCTTCCTTCTTGCTGGCTCATGCTTTGCTGGGCTCTGAGTTCCCAGTCATCTCGCAGACAGACAGTCAATAACTGGAGAAGAGTGTCCTAAACACAGCATCGCATCGCTCAGCCCTTCCTCACTAGTACTGTGACCTACTCTGACGTCTTAGTACTTGGTAGGTAGAGGCGGGAGCCCAAAAATAGCCTCCTGTACACAGTAAATTAGTAGTCAGCCTGGGCTACATGAAATCCTGTGTCAAAAAAAAAAAAAAATAAGGGGTGGGGGCTGTAGCTCAGTAAGTTGAGCCCTTGCCCAGGAGTTGTGGTAGACACCTGTCATCCCAGCCACTAGGCTGGGTTGAGGCAGGAGGATCAAGAGTTCAATATCATCCTACGCTACCTAGTGAAATTTCAGGCTAGCCTGGGCTTTTGAAGACACTGCATAAAAATATATATATACACATACATACATACATACATACATACATACATACATACATACATACAATTTTAAGACAGCAAGTCAAAAAAGCTATTCAACCCTTCCCATCACCTCCATCACCAAACAAACAATAGGCCAGGCAACATGGTTCCTCCAGGGCTTATGGCCAAGCAAGCTGGACAACACAAGTGTGACCTCTGGAAGAGCAGTCAGTGCTCTTGACCGCTGAGCCACCTCTCCAGCCCATAAAATGGTTTTTAATGTTTTAAAACAATAACAACAGAAAGGACAATCTATTTATTTCCCCTCTTCCCCATCCTCTAG
Seq C2 exon
TTCTGGGAGGTCATCAGTGATGAGCATGGCATCGACCCCACTGGGACCTATCATGGGGACAGTGACCTCCAGCTGGAGAGAATTAATGTCTACTACAACGAGGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000047505:ENSRNOT00000075767:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.189
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=PU(14.8=84.2)
A:
NA
C2:
PF0009120=Tubulin=FE(16.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCGCAGAGACAGAGCTCT
R:
TGTGGCCTCGTTGTAGTAGACA
Band lengths:
263-1331
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]